Funding & Acknowledgements

The data used in this analysis is from the Export Standardized Tables in the SEACAR Data Discovery Interface (DDI). Documents and information available through the SEACAR DDI are owned by the data provider(s) and users are expected to provide appropriate credit following accepted citation formats. Users are encouraged to access data to maximize utilization of gained knowledge, reducing redundant research and facilitating partnerships and scientific innovation.

With respect to documents and information available from SEACAR DDI, neither the State of Florida nor the Florida Department of Environmental Protection makes any warranty, expressed or implied, including the warranties of merchantability and fitness for a particular purpose arising out of the use or inability to use the data, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.

This report was funded in part, through a grant agreement from the Florida Department of Environmental Protection, Florida Coastal Management Program, by a grant provided by the Office for Coastal Management under the Coastal Zone Management Act of 1972, as amended, National Oceanic and Atmospheric Administration. The views, statements, findings, conclusions and recommendations expressed herein are those of the author(s) and do not necessarily reflect the views of the State of Florida, NOAA or any of their sub agencies.

Published: 2025-05-22

Threshold Filtering

Threshold filters, following the guidance of Florida Department of Environmental Protection’s (FDEP) Division of Environmental Assessment and Restoration (DEAR) are used to exclude specific results values from the SEACAR Analysis. Based on the threshold filters, Quality Assurance / Quality Control (QAQC) Flags are inserted into the SEACAR_QAQCFlagCode and SEACAR_QAQC_Description columns of the export data. The Include column indicates whether the QAQC Flag will also indicate that data are excluded from analysis. No data are excluded from the data export, but the analysis scripts can use the Include column to exclude data (1 to include, 0 to exclude).

Continuous Water Quality threshold values
Parameter Name Units Low Threshold High Threshold
Dissolved Oxygen mg/L -0.000001 50
Dissolved Oxygen Saturation % -0.000001 500
Salinity ppt -0.000001 70
Turbidity NTU -0.000001 4000
Water Temperature Degrees C -5.000000 45
pH None 2.000000 14
Discrete Water Quality threshold values
Parameter Name Units Low Threshold High Threshold
Ammonia, Un-ionized (NH3) mg/L - -
Ammonium, Filtered (NH4) mg/L - -
Chlorophyll a, Corrected for Pheophytin ug/L - -
Chlorophyll a, Uncorrected for Pheophytin ug/L - -
Colored Dissolved Organic Matter PCU - -
Dissolved Oxygen mg/L -0.000001 25
Dissolved Oxygen Saturation % -0.000001 310
Fluorescent Dissolved Organic Matter QSE - -
Light Extinction Coefficient m^-1 - -
NO2+3, Filtered mg/L - -
Nitrate (NO3) mg/L - -
Nitrite (NO2) mg/L - -
Nitrogen, organic mg/L - -
Phosphate, Filtered (PO4) mg/L - -
Salinity ppt -0.000001 70
Secchi Depth m 0.000001 50
Specific Conductivity mS/cm 0.005000 100
Total Kjeldahl Nitrogen mg/L - -
Total Nitrogen mg/L - -
Total Nitrogen mg/L - -
Total Phosphorus mg/L - -
Total Suspended Solids mg/L - -
Turbidity NTU - -
Water Temperature Degrees C 3.000000 40
pH None 2.000000 13
Quality Assurance Flags inserted based on threshold checks listed in Table 1 and 2
SEACAR QAQC Description Include SEACAR QAQCFlagCode
Exceeds maximum threshold 0 2Q
Below minimum threshold 0 4Q
Within threshold tolerance 1 6Q
No defined thresholds for this parameter 1 7Q

Value Qualifiers

Value qualifier codes included within the data are used to exclude certain results from the analysis. The data are retained in the data export files, but the analysis uses the Include column to filter the results.

STORET and WIN value qualifier codes

Value qualifier codes from STORET and WIN data are examined with the database and used to populate the Include column in data exports.

Value Qualifier codes excluded from analysis
Qualifier Source Value Qualifier Include MDL Description
STORET-WIN H 0 0 Value based on field kit determination; results may not be accurate
STORET-WIN J 0 0 Estimated value
STORET-WIN V 0 0 Analyte was detected at or above method detection limit
STORET-WIN Y 0 0

Discrete Water Quality Value Qualifiers

The following value qualifiers are highlighted in the Discrete Water Quality section of this report. An exception is made for Program 476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network and data flagged with Value Qualifier H are included for this program only.

H - Value based on field kit determiniation; results may not be accurate. This code shall be used if a field screening test (e.g., field gas chromatograph data, immunoassay, or vendor-supplied field kit) was used to generate the value and the field kit or method has not been recognized by the Department as equivalent to laboratory methods.

I - The reported value is greater than or equal to the laboratory method detection limit but less than the laboratory practical quantitation limit.

Q - Sample held beyond the accepted holding time. This code shall be used if the value is derived from a sample that was prepared or analyzed after the approved holding time restrictions for sample preparation or analysis.

S - Secchi disk visible to bottom of waterbody. The value reported is the depth of the waterbody at the location of the Secchi disk measurement.

U - Indicates that the compound was analyzed for but not detected. This symbol shall be used to indicate that the specified component was not detected. The value associated with the qualifier shall be the laboratory method detection limit. Unless requested by the client, less than the method detection limit values shall not be reported

Systemwide Monitoring Program (SWMP) value qualifier codes

Value qualifier codes from the SWMP continuous program are examined with the database and used to populate the Include column in data exports. SWMP Qualifier Codes are indicated by QualifierSource=SWMP.

SWMP Value Qualifier codes
Qualifier Source Value Qualifier Include Description
SWMP -1 1 Optional parameter not collected
SWMP -2 0 Missing data
SWMP -3 0 Data rejected due to QA/QC
SWMP -4 0 Outside low sensor range
SWMP -5 0 Outside high sensor range
SWMP 0 1 Passed initial QA/QC checks
SWMP 1 0 Suspect data
SWMP 2 1 Reserved for future use
SWMP 3 1
SWMP 4 1 Historical: Pre-auto QA/QC
SWMP 5 1 Corrected data

Water Column

The water column habitat extends from the water’s surface to the bottom sediments, and it’s where fish, dolphins, crabs and people swim! So much life makes its home in the water column that the health of marine and coastal ecosystems, as well as human economies, depend on the condition of this vulnerable habitat. Local patterns of rainfall, temperature, winds and currents can rapidly change the condition of the water column, while global influences such as El Niño/La Niña, large-scale fluctuation in sea temperatures and climate change can have long-term effects. Inputs from the prosperity of our day-to-day lives including farming, mining and forestry, and emissions from power generation, automobiles and water treatment can also alter the health of the water column. Acting alone or together, each input can have complex and lasting effects on habitats and ecosystems.


SEACAR evaluates water column health with several essential parameters. These include nutrient surveys of nitrogen and phosphorus, and water quality assessments of salinity, dissolved oxygen, pH, and water temperature. Water clarity is evaluated with Secchi depth, turbidity, levels of chlorophyll a, total suspended solids, and colored dissolved organic matter. Additionally, the richness of nekton is indicated by the abundance of free-swimming fishes and macroinvertebrates like crabs and shrimps.

Seasonal Kendall-Tau Analysis

Indicators must have a minimum of five to ten years, depending on the habitat, of data within the geographic range of the analysis to be included in the analysis. Ten years of data are required for discrete parameters, and five years of data are required for continuous parameters. If there are insufficient years of data, the number of years of data available will be noted and labeled as “insufficient data to conduct analysis”. Further, for the preferred Seasonal Kendall-Tau test, there must be data from at least two months in common across at least two consecutive years within the RCP managed area being analyzed. Values that pass both of these tests will be included in the analysis and be labeled as Use_In_Analysis = TRUE. Any that fail either test will be excluded from the analyses and labeled as Use_In_Analysis = FALSE. The points for all Water Column plots displayed in this section are monthly averages. Trend significance will be denoted as “Significant Trend” (when p < 0.05), or “Non-significant Trend” (when p >= 0.05). Any parameters with insufficient data to perform Seasonal Kendall-Tau test will have their monthly averages plotted without a corresponding trend line.

Water Quality - Discrete

The following files were used in the discrete analysis:

  • Combined_WQ_WC_NUT_Chlorophyll_a_corrected_for_pheophytin-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Chlorophyll_a_uncorrected_for_pheophytin-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Colored_dissolved_organic_matter_CDOM-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Dissolved_Oxygen-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Dissolved_Oxygen_Saturation-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_pH-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Salinity-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Secchi_Depth-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Total_Nitrogen-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Total_Phosphorus-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Total_Suspended_Solids_TSS-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Turbidity-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Water_Temperature-2025-Mar-06.txt

Chlorophyll a, Corrected for Pheophytin - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average levels of chlorophyll a, corrected for pheophytin, over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed chlorophyll a (triangles) is included in the plot.
Scatter plot of monthly average levels of chlorophyll a, corrected for pheophytin, over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed chlorophyll a (triangles) is included in the plot.
Seasonal Kendall-Tau Trend Analysis for Chlorophyll a, Corrected for Pheophytin
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab Significantly increasing trend 7492 25 2000 - 2024 8.6 0.2849 6.6053 0.2897 0

Monthly average chlorophyll a, corrected for pheophytin, increased by 0.29 µg/L per year, indicating a decrease in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Chlorophyll a, Corrected for Pheophytin
ProgramID N_Data YearMin YearMax
355 7101 2002 2024
5002 497 2000 2024

Program names:

355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
5002 - Florida STORET / WIN2

Chlorophyll a, Uncorrected for Pheophytin - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average levels of chlorophyll a, uncorrected for pheophytin, over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed chlorophyll a (triangles) is included in the plot.
Scatter plot of monthly average levels of chlorophyll a, uncorrected for pheophytin, over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed chlorophyll a (triangles) is included in the plot.
Seasonal Kendall-Tau Trend Analysis for Chlorophyll a, Uncorrected for Pheophytin
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab Significantly increasing trend 3967 21 2002 - 2024 11.65 0.1685 11.7621 0.249 0.0027

Monthly average chlorophyll a, uncorrected for pheophytin, increased by 0.25 µg/L per year, indicating a decrease in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Chlorophyll a, Uncorrected for Pheophytin
ProgramID N_Data YearMin YearMax
355 3975 2007 2024
5002 61 2012 2024
514 51 2007 2008
103 26 2002 2021
118 5 2005 2010
115 2 2002 2004

Program names:

103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX3
115 - Environmental Monitoring Assessment Program4
118 - National Aquatic Resource Surveys, National Coastal Condition Assessment5
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
514 - Florida LAKEWATCH Program6
5002 - Florida STORET / WIN2

Dissolved Oxygen - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average dissolved oxygen over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only dissolved oxygen values measured in the field (circles) are included in the plot.
Scatter plot of monthly average dissolved oxygen over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only dissolved oxygen values measured in the field (circles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Dissolved Oxygen
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly decreasing trend 52445 33 1992 - 2024 7.5 -0.1365 7.728 -0.0167 0.0003

Monthly average dissolved oxygen decreased by 0.02 mg/L per year.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Dissolved Oxygen
ProgramID N_Data YearMin YearMax
69 24593 1998 2022
5002 21942 1995 2024
129 3505 2000 2024
355 2963 2003 2024
95 256 1995 2018
557 121 2006 2023
118 52 2005 2020
103 22 2004 2021
115 16 1992 2004
119 14 1994 1994
5071 3 2017 2017

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program7
95 - Harmful Algal Bloom Marine Observation Network8
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX3
115 - Environmental Monitoring Assessment Program4
118 - National Aquatic Resource Surveys, National Coastal Condition Assessment5
119 - National Status and Trends Bioeffects program9
129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring10
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring11
5002 - Florida STORET / WIN2
5071 - Oyster shell heights and taxonomic diversity in 2015-2017 among previously documented oiled and non-oiled reefs in Louisiana, Alabama, and the Florida panhandle12

Dissolved Oxygen Saturation - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average dissolved oxygen saturation over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only dissolved oxygen saturation values measured in the field (circles) are included in the plot.
Scatter plot of monthly average dissolved oxygen saturation over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only dissolved oxygen saturation values measured in the field (circles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Dissolved Oxygen Saturation
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly increasing trend 5540 25 2000 - 2024 92.75 0.2129 88.1057 0.3508 0

Monthly average dissolved oxygen saturation increased by 0.35% per year.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Dissolved Oxygen Saturation
ProgramID N_Data YearMin YearMax
129 3491 2000 2024
355 1935 2003 2023
5002 141 2003 2024

Program names:

129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring10
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
5002 - Florida STORET / WIN2

pH - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average pH over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only pH values measured in the field (circles) are included in the plot.
Scatter plot of monthly average pH over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only pH values measured in the field (circles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for pH
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly decreasing trend 40959 34 1964 - 2024 8 -0.2769 8.2218 -0.0082 0

Monthly average pH decreased by 0.01 pH units per year.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for pH
ProgramID N_Data YearMin YearMax
69 24644 1998 2022
5002 12904 1995 2024
129 2063 2000 2024
355 2009 2011 2024
95 184 1964 2018
557 110 2006 2023
103 19 2004 2021
115 16 1992 2004

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program7
95 - Harmful Algal Bloom Marine Observation Network8
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX3
115 - Environmental Monitoring Assessment Program4
129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring10
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring11
5002 - Florida STORET / WIN2

Salinity - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average salinity over time. If the time series included ten or more years of discrete observations, significant (blue) or non-significant (magenta) trend lines are also shown. Discrete salinity values derived from grab samples analyzed in the field (circles) or the laboratory (triangles) are both included in the plot.
Scatter plot of monthly average salinity over time. If the time series included ten or more years of discrete observations, significant (blue) or non-significant (magenta) trend lines are also shown. Discrete salinity values derived from grab samples analyzed in the field (circles) or the laboratory (triangles) are both included in the plot.
Seasonal Kendall-Tau Trend Analysis for Salinity
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
All Significantly decreasing trend 61449 36 1964 - 2024 15.8 -0.1165 20.933 -0.0914 0.0023

Monthly average salinity decreased by 0.09 ppt per year.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Salinity
ProgramID N_Data YearMin YearMax
5002 30348 1995 2024
69 24742 1998 2022
129 3510 2000 2024
355 2923 2003 2024
95 373 1964 2018
4044 280 2007 2023
557 121 2006 2023
118 57 2015 2020
456 33 2005 2013
115 16 1992 2004
119 14 1994 1994
5071 3 2017 2017
103 3 2004 2004

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program7
95 - Harmful Algal Bloom Marine Observation Network8
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX3
115 - Environmental Monitoring Assessment Program4
118 - National Aquatic Resource Surveys, National Coastal Condition Assessment5
119 - National Status and Trends Bioeffects program9
129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring10
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
456 - Oyster Sentinel13
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring11
4044 - NRDA Oyster Cultch Recovery Project14
5002 - Florida STORET / WIN2
5071 - Oyster shell heights and taxonomic diversity in 2015-2017 among previously documented oiled and non-oiled reefs in Louisiana, Alabama, and the Florida panhandle12

Secchi Depth - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average Secchi depth over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Secchi depth is only measured in the field (circles).
Scatter plot of monthly average Secchi depth over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Secchi depth is only measured in the field (circles).
Seasonal Kendall-Tau Trend Analysis for Secchi Depth
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly increasing trend 27112 30 1992 - 2024 -0.8 0.103 -0.8483 0.0027 0.0151

Monthly average Secchi depth became shallower by less than 0.01 m per year, indicating a decrease in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Secchi Depth
ProgramID N_Data YearMin YearMax
69 24458 1998 2022
129 1734 2000 2024
355 731 2011 2019
557 67 2006 2023
5002 58 2012 2024
514 48 2007 2008
103 10 2021 2021
115 6 1992 2004

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program7
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX3
115 - Environmental Monitoring Assessment Program4
129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring10
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
514 - Florida LAKEWATCH Program6
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring11
5002 - Florida STORET / WIN2

Total Nitrogen - Discrete

Total Nitrogen Calculation:

The logic for calculated Total Nitrogen was provided by Kevin O’Donnell and colleagues at FDEP (with the help of Jay Silvanima, Watershed Monitoring Section). The following logic is used, in this order, based on the availability of specific nitrogen components.

  1. TN = TKN + NO3O2;
  2. TN = TKN + NO3 + NO2;
  3. TN = ORGN + NH4 + NO3O2;
  4. TN = ORGN + NH4 + NO2 + NO3;
  5. TN = TKN + NO3;
  6. TN = ORGN + NH4 + NO3;

Additional Information:

  • Rules for use of sample fraction:
    • Florida Department of Environmental Protection (FDEP) report that if both “Total” and “Dissolved” components are reported, only “Total” is used. If the total is not reported, then the dissolved components are used as a best available replacement.
    • Total nitrogen calculations are done using nitrogen components with the same sample fraction, nitrogen components with mixed total/dissolved sample fractions are not used. In other words, total nitrogen can be calculated when TKN and NO3O2 are both total sample fractions, or when both are dissolved sample fractions. Future calculations of total nitrogen values may be based on components with mixed sample fractions.
  • Values inserted into data:
    • ParameterName = “Total Nitrogen”
    • SEACAR_QAQCFlagCode = “1Q”
    • SEACAR_QAQC_Description = “SEACAR Calculated”

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average total nitrogen over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only nitrogen values obtained from laboratory analyses (triangles) are included in the plot.
Scatter plot of monthly average total nitrogen over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only nitrogen values obtained from laboratory analyses (triangles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Total Nitrogen
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab Significantly increasing trend 3242 23 1992 - 2024 0.62 0.1401 0.5553 0.0037 0.0099

Monthly average total nitrogen increased by less than 0.01 mg/L per year.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Total Nitrogen
ProgramID N_Data YearMin YearMax
355 2774 2013 2024
5002 418 1992 2024
514 50 2007 2008
103 15 2002 2006
115 2 2002 2004

Program names:

103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX3
115 - Environmental Monitoring Assessment Program4
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
514 - Florida LAKEWATCH Program6
5002 - Florida STORET / WIN2

Total Phosphorus - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average total phosphorus over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only phosphorus values obtained from laboratory analyses (triangles) are included in the plot.
Scatter plot of monthly average total phosphorus over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only phosphorus values obtained from laboratory analyses (triangles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Total Phosphorus
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab No significant trend 3531 23 1992 - 2024 0.031 0.046 0.027 0.0001 0.4992

Total phosphorus showed no detectable trend between 1992 and 2024.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Total Phosphorus
ProgramID N_Data YearMin YearMax
355 3046 2013 2024
5002 494 1992 2024
514 50 2007 2008
103 20 2002 2021
115 2 2002 2004

Program names:

103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX3
115 - Environmental Monitoring Assessment Program4
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
514 - Florida LAKEWATCH Program6
5002 - Florida STORET / WIN2

Total Suspended Solids - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average total suspended solids (TSS) over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only TSS values obtained from laboratory analyses (triangles) are included in the plot.
Scatter plot of monthly average total suspended solids (TSS) over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only TSS values obtained from laboratory analyses (triangles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Total Suspended Solids
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab No significant trend 3102 16 1992 - 2024 9 -0.0112 12.3358 -0.0439 0.754

Total suspended solids showed no detectable trend between 1992 and 2024.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Total Suspended Solids
ProgramID N_Data YearMin YearMax
355 3136 2013 2024
5002 117 1992 2024
103 10 2021 2021

Program names:

103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX3
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
5002 - Florida STORET / WIN2

Turbidity - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average turbidity over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only turbidity values measured in the laboratory (triangles) are included in the plot.
Scatter plot of monthly average turbidity over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only turbidity values measured in the laboratory (triangles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Turbidity
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab No significant trend 15518 27 1992 - 2024 5.6 -0.0259 6.4878 -0.0119 0.6339

Turbidity showed no detectable trend between 1992 and 2024.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Turbidity
ProgramID N_Data YearMin YearMax
5002 15520 1992 2024
129 2042 2000 2024
355 1446 2004 2019
4044 112 2021 2023
557 41 2022 2023
103 13 2005 2021

Program names:

103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX3
129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring10
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring11
4044 - NRDA Oyster Cultch Recovery Project14
5002 - Florida STORET / WIN2

Water Temperature - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average water temperature over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only water temperature measurements taken in the field (circles) are included in the plot.
Scatter plot of monthly average water temperature over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only water temperature measurements taken in the field (circles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Water Temperature
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly increasing trend 61315 36 1964 - 2024 24 0.0886 20.6039 0.0186 0.0226

Monthly average water temperature increased by 0.02°C per year.

Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Water Temperature
ProgramID N_Data YearMin YearMax
5002 30496 1995 2024
69 24833 1998 2022
129 3504 2000 2024
355 2965 2003 2024
95 332 1964 2018
557 121 2006 2023
456 33 2005 2013
103 20 2004 2021
115 16 1992 2004
119 14 1994 1994
5071 3 2017 2017

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program7
95 - Harmful Algal Bloom Marine Observation Network8
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX3
115 - Environmental Monitoring Assessment Program4
119 - National Status and Trends Bioeffects program9
129 - Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring10
355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1
456 - Oyster Sentinel13
557 - Central Panhandle Aquatic Preserves Seagrass Monitoring11
5002 - Florida STORET / WIN2
5071 - Oyster shell heights and taxonomic diversity in 2015-2017 among previously documented oiled and non-oiled reefs in Louisiana, Alabama, and the Florida panhandle12

Water Quality - Continuous

The following files were used in the continuous analysis:

  • Combined_WQ_WC_NUT_cont_Dissolved_Oxygen_NW-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Dissolved_Oxygen_Saturation_NW-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_pH_NW-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Salinity_NW-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Turbidity_NW-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Water_Temperature_NW-2025-Mar-06.txt

Continuous monitoring locations in Apalachicola Bay Aquatic Preserve

Station overview for Continuous parameters by Program
ProgramID ProgramLocationID Years of Data Use in Analysis Parameters
355 apadbwq 24 TRUE DO , DOS , pH , Sal , Turb , TempW
355 apaebwq 29 TRUE Turb
355 apaebwq 31 TRUE DO , DOS , pH , Sal , TempW
355 apaeswq 30 TRUE Turb
355 apaeswq 31 TRUE DO , DOS , pH , Sal , TempW
355 apalmwq 10 TRUE DO , DOS , pH , Sal , Turb , TempW
355 apapcwq 10 TRUE DO , DOS , pH , Sal , Turb , TempW

Program names:

355 - Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program1

Map showing continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. Sites marked as Use In Analysis (green) are featured in this report.
Map showing continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. Sites marked as Use In Analysis (green) are featured in this report.

Dissolved Oxygen - Continuous

Scatter plot of monthly average dissolved oxygen over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average dissolved oxygen over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Dissolved Oxygen - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
apaebwq Significantly decreasing trend 665356 31 1995 - 2025 6.8 -0.28 7.57 -0.06 0.00
apaeswq Significantly decreasing trend 715193 31 1995 - 2025 6.8 -0.15 7.21 -0.03 0.00
apapcwq No significant trend 267810 10 2016 - 2025 6.9 0.07 6.66 0.02 0.35
apadbwq Significantly decreasing trend 621272 24 2002 - 2025 7.3 -0.15 7.50 -0.02 0.00
apalmwq Significantly decreasing trend 255049 10 2016 - 2025 6.3 -0.22 6.94 -0.06 0.01

At four program locations, monthly average dissolved oxygen decreased between 0.02 and 0.06 mg/L per year. No detectable change in monthly average dissolved oxygen was observed at one location.

Map showing location of dissolved oxygen continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of dissolved oxygen continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Dissolved Oxygen Saturation - Continuous

Scatter plot of monthly average dissolved oxygen saturation over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average dissolved oxygen saturation over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Dissolved Oxygen Saturation - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
apadbwq Significantly decreasing trend 624721 24 2002 - 2025 94.7 -0.10 97.83 -0.15 0.02
apaeswq Significantly decreasing trend 716357 31 1995 - 2025 84.2 -0.11 86.07 -0.26 0.00
apaebwq Significantly decreasing trend 661181 31 1995 - 2025 84.8 -0.25 91.06 -0.67 0.00
apapcwq No significant trend 271266 10 2016 - 2025 94.1 0.11 92.05 0.35 0.16
apalmwq Significantly decreasing trend 255585 10 2016 - 2025 74.7 -0.22 78.57 -0.75 0.01

At four program locations, monthly average dissolved oxygen saturation decreased between 0.15 and 0.75% per year. No detectable change in monthly average dissolved oxygen saturation was observed at one location.

Map showing location of dissolved oxygen saturation continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of dissolved oxygen saturation continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

pH - Continuous

Scatter plot of monthly average pH over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average pH over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for pH - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
apadbwq Significantly decreasing trend 602330 24 2002 - 2025 8.0 -0.14 8.06 0.00 0.00
apalmwq No significant trend 263183 10 2016 - 2025 7.1 -0.07 7.16 -0.01 0.43
apaebwq Significantly decreasing trend 717948 31 1995 - 2025 7.6 -0.11 7.64 -0.01 0.00
apaeswq Significantly decreasing trend 719429 31 1995 - 2025 7.5 -0.12 7.58 -0.01 0.00
apapcwq Significantly decreasing trend 267739 10 2016 - 2025 8.1 -0.28 8.16 -0.01 0.00

At four program locations, monthly average pH decreased between less than 0.01 and 0.01 pH units per year. No detectable change in monthly average pH was observed at one location.

Map showing location of ph continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of ph continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Salinity - Continuous

Scatter plot of monthly average salinity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average salinity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Salinity - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
apaeswq No significant trend 759370 31 1995 - 2025 7.6 0.05 6.93 0.03 0.17
apaebwq No significant trend 747149 31 1995 - 2025 9.9 0.04 9.14 0.02 0.31
apadbwq No significant trend 619355 24 2002 - 2025 22.1 -0.03 22.34 -0.03 0.44
apalmwq Significantly increasing trend 270761 10 2016 - 2025 0.1 0.23 0.09 0.01 0.01
apapcwq No significant trend 270115 10 2016 - 2025 26.8 0.03 26.46 0.07 0.70

At one program location, monthly average salinity increased by 0.01 ppt per year. No detectable change in monthly average salinity was observed at four locations.

Map showing location of salinity continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of salinity continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Turbidity - Continuous

Scatter plot of monthly average turbidity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average turbidity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Turbidity - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
apaeswq Significantly decreasing trend 703229 30 1996 - 2025 9 -0.15 11.32 -0.11 0.00
apapcwq No significant trend 258576 10 2016 - 2025 7 -0.03 10.47 -0.03 0.78
apaebwq Significantly decreasing trend 635704 27 1997 - 2025 13 -0.19 19.68 -0.19 0.00
apadbwq No significant trend 605643 24 2002 - 2025 10 0.04 16.11 0.05 0.32
apalmwq Significantly increasing trend 245206 10 2016 - 2025 12 0.20 7.63 0.70 0.02

At one program location, monthly average turbidity increased by 0.70 NTU per year. At two program locations, monthly average turbidity decreased by 0.11 NTU per year at one site and by 0.19 NTU per year at the other. No detectable change in monthly average turbidity was observed at two locations.

Map showing location of turbidity continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of turbidity continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Water Temperature - Continuous

Scatter plot of monthly average water temperature over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average water temperature over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Water Temperature - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
apadbwq Significantly increasing trend 644531 24 2002 - 2025 23.3 0.14 22.90 0.03 0.00
apaeswq Significantly increasing trend 768616 31 1995 - 2025 24.2 0.19 22.80 0.04 0.00
apalmwq No significant trend 273020 10 2016 - 2025 22.6 -0.03 23.64 -0.02 0.70
apaebwq Significantly increasing trend 762203 31 1995 - 2025 24.2 0.15 23.07 0.02 0.00
apapcwq No significant trend 273607 10 2016 - 2025 23.1 -0.06 23.68 -0.03 0.47

At three program locations, monthly average water temperature increased between 0.02 and 0.04°C per year. No detectable change in monthly average water temperature was observed at two locations.

Map showing location of water temperature continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of water temperature continuous water quality sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Submerged Aquatic Vegetation

The data file used is: All_SAV_Parameters-2025-Mar-06.txt

Submerged aquatic vegetation (SAV) refers to plants and plant-like macroalgae species that live entirely underwater. The two primary categories of SAV inhabiting Florida estuaries are benthic macroalgae and seagrasses. They often grow together in dense beds or meadows that carpet the seafloor. Macroalgae include multicellular species of green, red and brown algae that often live attached to the substrate by a holdfast. They tend to grow quickly and can tolerate relatively high nutrient levels, making them a threat to seagrasses and other benthic habitats in areas with poor water quality. In contrast, seagrasses are grass-like, vascular, flowering plants that are attached to the seafloor by extensive root systems. Seagrasses occur throughout the coastal areas of Florida, including protected bays and lagoons as well as deeper offshore waters on the continental shelf. Seagrasses have taken advantage of the broad, shallow shelf and clear water to produce two of the most extensive seagrass beds anywhere in continental North America.

Parameters

Percent Cover measures the fraction of an area of seafloor that is covered by SAV, usually estimated by evaluating multiple small areas of seafloor. Percent cover is often estimated for total SAV, individual types of vegetation (seagrass, attached algae, drift algae) and individual species.

Frequency of Occurrence was calculated as the number of times a taxon was observed in a year divided by the number of sampling events, multiplied by 100. Analysis is conducted at the quadrat level and is inclusive of all quadrats (i.e., quadrats evaluated using Braun-Blanquet, modified Braun-Blanquet, and percent cover.”

Species

Turtle grass (Thalassia testudinum) is the largest of the Florida seagrasses, with longer, thicker blades and deeper root structures than any of the other seagrasses. It is considered a climax seagrass species.

Shoal grass (Halodule wrightii) is an early colonizer of vegetated areas and usually grows in water too shallow for other species except widgeon grass. It can often tolerate larger salinity ranges than other seagrass species. Shoal grass is characterized by thin, flat blades, that are narrower than turtle grass blades.

Manatee grass (Syringodium filiforme) is easily recognizable because its leaves are thin and cylindrical instead of the flat, ribbon-like form shared by many other seagrass species. The leaves can grow up to half a meter in length. Manatee grass is usually found in mixed seagrass beds or small, dense monospecific patches.

Widgeon grass (Ruppia maritima) grows in both fresh and salt water and is widely distributed throughout Florida’s estuaries in less saline areas, particularly in inlets along the east coast. This species resembles shoal grass in certain environments but can be identified by the pointed tips of its leaves.

Three species of Halophila spp. are found in Florida - Star grass (Halophila engelmannii), Paddle grass (Halophila decipiens), and Johnson’s seagrass (Halophila johnsonii). These are smaller, more fragile seagrasses than other Florida species and are considered ephemeral. They grow along a single long rhizome, with short blades. These species are not well-studied, although surveys are underway to define their ecological roles.

Notes

Star grass, Paddle grass, and Johnson’s seagrass will be grouped together and listed as Halophila spp. in the following managed areas. This is because several surveys did not specify to the species level:

  • Banana River Aquatic Preserve

  • Indian River-Malabar to Vero Beach Aquatic Preserve

  • Indian River-Vero Beach to Ft. Pierce Aquatic Preserve

  • Jensen Beach to Jupiter Inlet Aquatic Preserve

  • Loxahatchee River-Lake Worth Creek Aquatic Preserve

  • Mosquito Lagoon Aquatic Preserve

  • Biscayne Bay Aquatic Preserve

  • Florida Keys National Marine Sanctuary

Maps showing the temporal scope of SAV sampling sites within the boundaries of Apalachicola Bay Aquatic Preserve by Program name.
Maps showing the temporal scope of SAV sampling sites within the boundaries of Apalachicola Bay Aquatic Preserve by Program name.

Click here to view spatio-temporal plots on GitHub.

Sampling locations by Program:

Map showing SAV sampling sites within the boundaries of Apalachicola Bay Aquatic Preserve. The point size reflects the number of samples at a given sampling site.
Map showing SAV sampling sites within the boundaries of Apalachicola Bay Aquatic Preserve. The point size reflects the number of samples at a given sampling site.
Program Information for Submerged Aquatic Vegetation
ProgramID N-Data YearMin YearMax method Sample Locations
557 308 2008 2023 Braun Blanquet 21
997 79 2003 2003 Braun Blanquet 4
997 81 2003 2003 Percent Cover 4

Program names:

557 - Central Panhandle Aquatic Preserves Seagrass Monitoring11
997 - Apalachicola Bay Ephemeral SAV Monitoring15
997 - Apalachicola Bay Ephemeral SAV Monitoring15

Scatter plots of median percent cover of submerged aquatic vegetation over time by group. Plots for time series that included five or more years of observations show the estimated trend as a blue line.
Scatter plots of median percent cover of submerged aquatic vegetation over time by group. Plots for time series that included five or more years of observations show the estimated trend as a blue line.
Trends in median percent cover for various seagrass species in Apalachicola Bay Aquatic Preserve - simplified
Trends in median percent cover for various seagrass species in Apalachicola Bay Aquatic Preserve - simplified
Percent Cover Trend Analysis for Apalachicola Bay Aquatic Preserve
CommonName Trend Significance (0.05) Period of Record LME-Intercept LME-Slope p
Drift algae Significantly decreasing trend 2003 - 2023 84.82204 -2.6309660 0.0014346
Shoal grass No significant trend 2008 - 2023 31.68993 0.9163934 0.4876111
No grass in quadrat Model did not fit the available data 2003 - 2023 - - -
Widgeon grass Insufficient data to calculate trend - - - -

An annual decrease in percent cover was observed for drift algae (-2.6%). No detectable change in percent cover was observed for shoal grass. Trends in percent cover could not be evaluated for widgeon grass due to insufficient data.

Frequency of occurrence for various seagrass species in Apalachicola Bay Aquatic Preserve
Frequency of occurrence for various seagrass species in Apalachicola Bay Aquatic Preserve

Nekton

The data file used is: All_NEKTON_Parameters-2025-Mar-06.txt

Bar graph(s) of annual average nekton richness over time for species groups occurring in at least 1% of samples. The bar colors represent species groups including bony fishes, cartilaginous fishes, decapod crustaceans (e.g., shrimps, crabs, and lobsters), and cephalopods (e.g., squid). Gear types and sizes are indicated in the panel label.
Bar graph(s) of annual average nekton richness over time for species groups occurring in at least 1% of samples. The bar colors represent species groups including bony fishes, cartilaginous fishes, decapod crustaceans (e.g., shrimps, crabs, and lobsters), and cephalopods (e.g., squid). Gear types and sizes are indicated in the panel label.
Nekton Species Richness
Gear Type Sample Count Number of Years Period of Record Median N of Taxa Mean N of Taxa
Trawl (4.8) 4967 24 2000 - 2024 0.74 1.13

The median annual number of taxa was 0.74 based on 4,967 observations collected by 4.8-meter trawl between 2000 and 2024.

Map showing location of nekton sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of nekton sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Coastal Wetlands

The data file used is: All_CW_Parameters-2025-Mar-06.txt

Line graph of annual average coastal wetlands species richness over time for mangroves and associates (triangles), marsh (squares), and marsh succulents (circles). If the time series by species group included more than one year of observations, a line connects data points for visualization.
Line graph of annual average coastal wetlands species richness over time for mangroves and associates (triangles), marsh (squares), and marsh succulents (circles). If the time series by species group included more than one year of observations, a line connects data points for visualization.
Coastal Wetlands Species Richness
Species Group Sample Count Number of Years Period of Record Median N of Taxa Mean N of Taxa
Mangroves and associates 4 2 2022 - 2023 1.0 1.00
Marsh 144 10 2014 - 2023 1.5 2.08
Marsh succulents 56 10 2014 - 2023 3.0 2.20

Between 2022 and 2023, the median annual number of species for mangroves and associates was 1 based on 4 observations. Between 2014 and 2023, the median annual number of species for marsh was 1.5 based on 144 observations. Between 2014 and 2023, the median annual number of species for marsh succulents was 3 based on 56 observations.

Map showing location of coastal wetlands sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of coastal wetlands sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Oyster

The data file used is: All_OYSTER_Parameters-2025-Apr-24.txt

Density

Natural

Scatter plot of oyster density over time. If the time series included five or more years with observations, an estimated trend (blue line) and a 95% credible interval (purple band) may also be plotted. Data points are jittered horizontally to reduce overlap.
Scatter plot of oyster density over time. If the time series included five or more years with observations, an estimated trend (blue line) and a 95% credible interval (purple band) may also be plotted. Data points are jittered horizontally to reduce overlap.
Model results for Oyster Density - Natural
Shell Type Habitat Type Trend Status Estimate Standard Error Credible Interval
Live Oysters Natural Significantly decreasing trend -7 43.4 -0.13 to -267.35

For natural reefs, density decreased by an average of 7 oysters per square meter per year. For restored reefs, density decreased by an average of 6.01 oysters per square meter per year.

Restored

Scatter plot of oyster density over time. If the time series included five or more years with observations, an estimated trend (blue line) and a 95% credible interval (purple band) may also be plotted. Data points are jittered horizontally to reduce overlap.
Scatter plot of oyster density over time. If the time series included five or more years with observations, an estimated trend (blue line) and a 95% credible interval (purple band) may also be plotted. Data points are jittered horizontally to reduce overlap.
Model results for Oyster Density - Restored
Shell Type Habitat Type Trend Status Estimate Standard Error Credible Interval
Live Oysters Restored No significant change -6.01 27.49 -0.05 to 33.37

For natural reefs, density decreased by an average of 7 oysters per square meter per year. For restored reefs, density decreased by an average of 6.01 oysters per square meter per year.

Map showing location of oyster density sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of oyster density sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Percent Live

Natural

Scatter plot of percent live oysters over time. If the time series included five or more years with observations, an estimated trend (blue line) and a 95% credible interval (purple band) may also be plotted. Data points are jittered horizontally to reduce overlap.
Scatter plot of percent live oysters over time. If the time series included five or more years with observations, an estimated trend (blue line) and a 95% credible interval (purple band) may also be plotted. Data points are jittered horizontally to reduce overlap.
Model results for Oyster Percent Live - Natural
Shell Type Habitat Type Trend Status Estimate Standard Error Credible Interval
Live Oysters Natural Significantly increasing trend 0.75 2.38 0 to 6.79

For natural reefs, percent live cover increased by an average of 0.75% per year. For restored reefs, percent live cover decreased by an average of 2.12% per year.

Restored

Scatter plot of percent live oysters over time. If the time series included five or more years with observations, an estimated trend (blue line) and a 95% credible interval (purple band) may also be plotted. Data points are jittered horizontally to reduce overlap.
Scatter plot of percent live oysters over time. If the time series included five or more years with observations, an estimated trend (blue line) and a 95% credible interval (purple band) may also be plotted. Data points are jittered horizontally to reduce overlap.
Model results for Oyster Percent Live - Restored
Shell Type Habitat Type Trend Status Estimate Standard Error Credible Interval
Live Oysters Restored Significantly decreasing trend -2.12 36.27 -1.39 to -0.53

For natural reefs, percent live cover increased by an average of 0.75% per year. For restored reefs, percent live cover decreased by an average of 2.12% per year.

Map showing location of oyster percent live sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of oyster percent live sampling locations within the boundaries of Apalachicola Bay Aquatic Preserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

References

1.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Apalachicola National Estuarine Research Reserve. Apalachicola National Estuarine Research Reserve System-Wide Monitoring Program. (2024).
2.
Florida Department of Environmental Protection (DEP). Florida STORET / WIN. (2024).
3.
U.S. Environmental Protection Agency (EPA). EPA STOrage and RETrieval Data Warehouse (STORET)/WQX. (2023).
4.
U.S. Environmental Protection Agency (EPA); Office of Research and Development. Environmental Monitoring Assessment Program. (2004).
5.
U.S. Environmental Protection Agency (EPA); Office of Water; National Oceanic and Atmospheric Administration (NOAA); U.S. Geological Survey (USGS); U.S. Fish and Wildlife Service (USFWS); National Estuary Program (NEP); coastal states. National Aquatic Resource Surveys, National Coastal Condition Assessment. (2021).
6.
University of Florida (UF); Institute of Food and Agricultural Sciences. Florida LAKEWATCH Program. (2024).
7.
Florida Fish and Wildlife Conservation Commission (FWC). Fisheries-Independent Monitoring (FIM) Program. (2022).
8.
Florida Fish and Wildlife Conservation Commission (FWC); Florida Fish and Wildlife Research Institute (FWRI). Harmful Algal Bloom Marine Observation Network. (2018).
9.
National Oceanic and Atmospheric Administration (NOAA); National Centers for Coastal Ocean Science’s Center for Coastal Monitoring and Assessment. National Status and Trends Bioeffects program. (1994).
10.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Apalachicola National Estuarine Research Reserve. Apalachicola National Estuarine Research Reserve Juvenile Fish and Benthic Macroinvertebrate Monitoring. (2023).
11.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Central Panhandle Aquatic Preserves. Central Panhandle Aquatic Preserves Seagrass Monitoring. (2023).
12.
Alabama Center for Ecological Resilience (ACER). Oyster shell heights and taxonomic diversity in 2015-2017 among previously documented oiled and non-oiled reefs in Louisiana, Alabama, and the Florida panhandle. (2017).
13.
Oyster Sentinel. Oyster Sentinel . (2016).
14.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Central Panhandle Aquatic Preserves. NRDA Oyster Cultch Recovery Project. (2024).
15.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Apalachicola National Estuarine Research Reserve. Apalachicola Bay Ephemeral SAV Monitoring. (2004).